I ran across a problem where if you download two copies of Eclipse (for example Juno with CDT and Juno with Java) and they point to the same workspace, an issue occurs where updates to code within the IDE that are saved are not recognized on build.

For example,

I could create a file, foo.cpp in a project in a workspace shared by two instances of eclipse. I edit the file foo.cpp to change a portion of the code. I save the code and do a clean build and run the new build of foo.cpp. The changes to foo.cpp will not be evident in the run. This problem is NOT remedied by restarting eclipse.

I am not sure if this counts as a bug for report. I was able to reproduce it.